[R] Correcting dates in research / medical record using R

PIKAL Petr
Wed, 12 Sep 2018 06:26:30 -0000

Hi

First of all you should not use HTML formated posts, it is big chance that it
gets scrambled.

You should compare your ld2 after for cycle and result of

clinicVdate[Id2, 'VisitDate'], sep=':')

Most probably ld2 after for cycle does not conform to row names of clinicVdate.

Cheers
Petr


> -----Original Message-----
> From: R-help <r-help-bounces at r-project.org> On Behalf Of Nicola
Cecchino
> Sent: Wednesday, September 12, 2018 3:50 AM
> To: R-help at r-project.org
> Subject: [R] Correcting dates in research / medical record using R
>
> Hi,
>
> I'm not that well versed with R - I'm trying to correct the dates
of
> service in a de-identified research medical record of several subjects.
> The correct dates come from a csv file, in the VisitDate column,  that
> looks like this in Excel.  The empty cells have other data in them that
> I don't need and the  file name is DateR.csv:
>
>
> Id1 Id2
>
>
>
>
> VisitDate
> 12345 12345
>
>
>
>
> 4/3/2018
>
>
> The research medical record is a text file and the "DATE OF
SERVICE" in
> the top matter is in error in all of the subjects and needs to be
> replaced with the "VisitDate" in the csv file.  The file name for
the
> medical records is test3.NEW.  Here is a screen grab of the top matter
> of the research medical record; below this data excerpt is other
> gathered data for that subject:
>
>
> ==================================================================>
============>
> PATIENT NAME: CONFIDENTIAL,#12345
> PATIENT ID #: 12345
> DATE OF SERVICE: 04/10/2018
> ACCESSION NUMBER: RR1234567
>
> TEST PROCEDURE        HIGH/LOW  TEST RESULTS       UNITS NORMAL VALUES
>
>
> As described above, I need to update the text file DATE OF SERVICE:
> date with the VisitDate in the csv file.
>
> I made several attempts at this to failure and so now I turn to you.
> Here is the code that exhibits my attempts:
>
>
> clinicVdate <- read.csv("DateR.csv")
>
> rownames(clinicVdate) <- as.character(clinicVdate[,'Id2'])
>
> Id2 <- NA
>
> input_data <- readLines("D:/test/test3.NEW")
> output_data <- c()
>
> for(input_line in input_data){
>    output_line = input_line
>    if(length(grep('PATIENT ID #:', input_line))>0)  {
>      Id2 = as.character(strsplit(input_line, ':')[[1]][2])
>    }
>
>    if (length(grep( 'DATE OF SERVICE: ', input_line))){
>
>      output_line = paste('DATE OF SERVICE', clinicVdate[Id2,
> 'VisitDate'], sep=':')
>
>    }
>    output_data = paste(output_data, output_line, sep='\n')
> }
>
> cat(output_data)
>
>
> The results of the above remove the erroneous date and replace it with
> NA.  Here is an example of the results:
>
>
> ==================================================================>
============>
> PATIENT NAME: CONFIDENTIAL,#12345
> PATIENT ID #: 12345
> DATE OF SERVICE: NA
> ACCESSION NUMBER: RR1234567
>
> TEST PROCEDURE        HIGH/LOW  TEST RESULTS       UNITS NORMAL VALUES
>
>
> Where am I going wrong?  If I didn't pose my question appropriately,
> please let me know too!!  Any help with this would be greatly appreciated!!
>
> Kind regards,
>
> Nic Cecchino
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch
partner? PRECHEZA a.s. jsou zve?ejn?ny na:
https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about
processing and protection of business partner?s personal data are available on
website: https://www.precheza.cz/en/personal-data-protection-principles/
D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a
podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? odpov?dnosti:
https://www.precheza.cz/01-dovetek/ | This email and any documents attached to
it may be confidential and are subject to the legally binding disclaimer: